Discovery of an In Vivo Chemical Probe for BCL6 Inhibition by Optimization of Tricyclic Quinolinones

Designed peptide binders and nanobodies as PROTAC starting points for targeted degradation of PCNA and BCL6

The efficient degradation of pathogenic proteins, particularly proliferating cell nuclear antigen (PCNA) and B-cell lymphoma 6 protein (BCL6), is crucial for treating various diseases related to cancer. As key biological macromolecules, PCNA plays a critical role in DNA replication and repair, while BCL6 acts as a transcriptional repressor involved in B-cell lymphoma. To enhance the efficiency and specificity of protein degradation, we developed a RS80E-based bioPROTACs system that consists of truncated variants of Ring-B-boxed coiled-coil (RBCC) domains (RS80E) with improved degradation efficiency fused to an AI-driven binder/nanobody targeting specific antigens. Combining state-of-the-art methodologies such as ProteinMPNN, RFdiffusion, AlphaFold3, AlphaFold2, and HADDOCK, we identified binders for PCNA and predicted spatial interrelationships. Employing fragment-based and alanine scanning methods, we designed nanobodies targeting PCNA and BCL6 by combinatorially designing CDR3 and grafting them onto nanobody scaffolds. Significantly, our results demonstrate the utility of bioPROTACs in degrading PCNA and BCL6, thereby activating p53 and promoting apoptosis. This highlights the therapeutic potential of targeting PCNA and BCL6 degradation and lays the groundwork for developing PCNA and BCL6-degrading therapeutics. In summary, our system offers a modular and rapid pathway for exploration other intractable therapeutic targets, and emphasizes the importance of interdisciplinary methods in advancing therapeutic interventions.

A Bivalent Molecular Glue Linking Lysine Acetyltransferases to Oncogene-induced Cell Death

Developing cancer therapies that induce robust death of the malignant cell is critical to prevent relapse. Highly effective strategies, such as immunotherapy, exemplify this observation. Here we provide the structural and molecular underpinnings for an approach that leverages chemical induced proximity to produce specific cell killing of diffuse large B cell lymphoma, the most common non-Hodgkin's lymphoma. We develop KAT-TCIPs (lysine acetyltransferase transcriptional/epigenetic chemical inducers of proximity) that redirect p300 and CBP to activate programmed cell death genes normally repressed by the oncogenic driver, BCL6. Acute treatment rapidly reprograms the epigenome to initiate apoptosis and repress c-MYC. The crystal structure of the chemically induced p300-BCL6 complex reveals how chance interactions between the two proteins can be systematically exploited to produce the exquisite potency and selectivity of KAT-TCIPs. Thus, the malignant function of an oncogenic driver can be co-opted to activate robust cell death, with implications for precision epigenetic therapies.

Discovery of novel BCL6-Targeting PROTACs with effective antitumor activities against DLBCL in vitro and in vivo

The transcriptional repressor B cell lymphoma 6 (BCL6) plays a critical role in driving tumorigenesis of diffuse large B-cell lymphoma (DLBCL). However, the therapeutic potential of inhibiting or degrading BCL6 for DLBCL has not been thoroughly understood. Herein, we reported the discovery of a series of novel BCL6-targeting PROTACs based on our previously reported N-phenyl-4-pyrimidinamine BCL6 inhibitors. The optimal compound DZ-837 degraded BCL6 with DC50 values around 600 nM and effectively inhibited the proliferation of several DLBCL cell lines. Further study indicated that DZ-837 induced significant G1 phase arrest and exhibited sustained reactivation of BCL6 downstream genes. In the SU-DHL-4 xenograft model, DZ-837 significantly inhibited tumor growth with TGI of 71.8 % at 40 mg/kg once daily. Furthermore, the combination of DZ-837 with BTK inhibitor Ibrutinib showed synergistic effects and overcame acquired resistance against DLBCL cells. Overall, our findings demonstrate that DZ-837 is an effective BCL6 degrader for DLBCL treatment as a monotherapy or in combination with Ibrutinib.